//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

#pragma once

#include "assembly/AssemblyReadInfo.hpp"
#include "options/IterativeAssemblerOptions.hpp"
#include "options/ReadScannerOptions.hpp"

typedef IterativeAssemblerOptions AssemblerOptions;

/// load all reads form bam into assembly input structure with minimal
/// filtration / input manipulation
///
void extractAssemblyReadsFromBam(
    const ReadScannerOptions& scanOpt,
    const AssemblerOptions&   asmOpt,
    const std::string&        referenceFilename,
    const std::string&        alignmentFilename,
    AssemblyReadInput&        reads);
